The use of VMD (Visual Molecular Dynamics) software for visualizing molecular simulations from a Web interface is described. Results from molecular simulation calculations are animated as a series of snapshots, each of which shows the positions and types of all atoms comprising the molecular system being simulated. Data for these snapshots are generated on a linux workstation and are sent to a PC on which VMD has been installed, and animated by VMD, either subsequently or as the simulation is being performed. Issues related to set-up and data sharing between different machines are described, as are a series of features added to the Web interface. For illustration, normal modes from the recently developed trajectory averaged normal coordinate analysis method are visualized.
|Presenter:||Subin Sindurakar (Undergraduate Student)|
|Time:||9 am (Session I)|